Looking at it Scott, I think you'll be doing a fair bit of beach fishing. The two estuaries near Thornton Beach have intrigued me for a while now, more on how to get in there in the boat. I don't know of a ramp nearby except for up Daintree, which I'm thinking of doing the run around to get in to. But I dare say there could be some success throwing spoons, slices into the mouth there from the bank.
Cooktown, if you have a search on here, there is a couple of threads on Cooktown, some give some good advice about fishing the jetty area.
Hann River Crossing. I've had limited success around this area over the years, but walking the banks flicking for Barra can be rewarding. We've always made sure that we've had someone on lizard watch though, back in the day Hann used to be where a lot of the 'rogue ' crocs were relocated to.
Chilli Beach, again, had limited luck throwing lures and plastics around the rocky area just in front of the camp grounds. Did head up to the headlands at the northern end of the beach, but got confronted with some locals that swiftly told me I wasn't allowed to be there. I wasn't sure if I was or not, there was a sign at the top of the beach but I figured it was for the buildings there not the beach and rocks, so I left anyway. Challenge here is the winds, if it's blowing, you'll be too busy holding the camp down to fish.
Bramwell, not much fishing to be had here, most of my trips north were before the roadhouse was built, you'll enjoy the hospitality and the food.
Elliot Falls, you'll be enjoying swimming too much to fish, and there's not a lot of fishing to be had in this area I don't believe.
Punsand Bay, ask the locals at the bar up there what's happening where, and where you can fish and where you can't. There's a lot of options around the cape, whether over the Eastern side around Somerset Bay, or Western Side. Will depend if you want to charter, or keep to land based. There are jettys around Seisia (but unless your staying there it's a fair hike from Punsand). Not sure if you're still allowed, but I've seen some great fish caught from the tip, the rocks near the sign. Again, the Eastern Side at that time of the year has a great chance of the winds making it difficult to throw anything but well weighted plastics or slices.
Cairns, join the Cairns fishing facebook pages, there's a lot of info on there about land based fishing, and some great guides around the Daintree and Port Douglas areas if you wanted to experience the Inshore GT fishing or the river Barra fishing. There a few threads on here for around Cairns as well, but most seem to have luck around the boardwalk and from some of the jetties at the boat ramps.
Hope this helps somewhat